Computational approaches on stoichiometric and kinetic modeling for efficient strain design

Mohammad Mazharul Islam, Rajib Saha

Research output: Chapter in Book/Report/Conference proceedingChapter

3 Citations (Scopus)

Abstract

Engineering biological systems that are capable of overproducing products of interest is the ultimate goal of any biotechnology application. To this end, stoichiometric (or steady state) and kinetic models are increasingly becoming available for a variety of organisms including prokaryotes, eukaryotes, and microbial communities. This ever-accelerating pace of such model reconstructions has also spurred the development of optimization-based strain design techniques. This chapter highlights a number of such frameworks developed in recent years in order to generate testable hypotheses (in terms of genetic interventions), thus addressing the challenges in metabolic engineering. In particular, three major methods are covered in detail including two methods for designing strains (i.e., one stoichiometric model-based and the other by integrating kinetic information into a stoichiometric model) and one method for analyzing microbial communities.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Pages63-82
Number of pages20
Volume1671
DOIs
StatePublished - Jan 1 2018

Publication series

NameMethods in Molecular Biology
Volume1671
ISSN (Print)1064-3745

Fingerprint

Metabolic Engineering
Bioengineering
Genetic Engineering
Biotechnology
Eukaryota

Keywords

  • Computational strain design
  • Ensemble modeling
  • Kinetic models
  • Metabolic modeling
  • Microbial communities
  • Multi-tissue model
  • Stoichiometric metabolic models
  • Whole plant model

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

Cite this

Islam, M. M., & Saha, R. (2018). Computational approaches on stoichiometric and kinetic modeling for efficient strain design. In Methods in Molecular Biology (Vol. 1671, pp. 63-82). (Methods in Molecular Biology; Vol. 1671). Humana Press Inc.. https://doi.org/10.1007/978-1-4939-7295-1_5

Computational approaches on stoichiometric and kinetic modeling for efficient strain design. / Islam, Mohammad Mazharul; Saha, Rajib.

Methods in Molecular Biology. Vol. 1671 Humana Press Inc., 2018. p. 63-82 (Methods in Molecular Biology; Vol. 1671).

Research output: Chapter in Book/Report/Conference proceedingChapter

Islam, MM & Saha, R 2018, Computational approaches on stoichiometric and kinetic modeling for efficient strain design. in Methods in Molecular Biology. vol. 1671, Methods in Molecular Biology, vol. 1671, Humana Press Inc., pp. 63-82. https://doi.org/10.1007/978-1-4939-7295-1_5
Islam MM, Saha R. Computational approaches on stoichiometric and kinetic modeling for efficient strain design. In Methods in Molecular Biology. Vol. 1671. Humana Press Inc. 2018. p. 63-82. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-4939-7295-1_5
Islam, Mohammad Mazharul ; Saha, Rajib. / Computational approaches on stoichiometric and kinetic modeling for efficient strain design. Methods in Molecular Biology. Vol. 1671 Humana Press Inc., 2018. pp. 63-82 (Methods in Molecular Biology).
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